[gmx-users] bad bond in polymer
nicegromacs
nicegromacs at live.cl
Fri Aug 14 20:31:59 CEST 2009
Hi Justin,
ups!! I am sorry this is the exact .pdb file.
HETATM 1 CAA DR0 1 83.043 46.127 36.820 1.00 0.00
HETATM 2 CAB DR0 1 82.411 45.765 35.421 1.00 0.00
HETATM 3 CAC DR0 1 81.495 46.822 34.598 1.00 0.00
HETATM 4 CAD DR0 1 80.621 46.369 33.071 1.00 0.00
HETATM 5 CAE DR0 1 79.305 47.302 32.172 1.00 0.00
HETATM 6 CAF DR0 1 77.939 46.749 31.124 1.00 0.00
HETATM 7 CAG DR0 1 76.264 47.439 30.612 1.00 0.00
HETATM 8 CAH DR0 1 74.636 46.805 29.962 1.00 0.00
HETATM 9 CAI DR0 1 72.805 47.674 30.179 1.00 0.00
HETATM 10 CAJ DR0 1 73.794 48.838 31.123 1.00 0.00
HETATM 11 OAK DR0 1 74.815 49.342 30.292 1.00 0.00
HETATM 12 OAL DR0 1 74.592 48.143 32.194 1.00 0.00
HETATM 13 CAM DR0 1 71.093 47.685 29.486 1.00 0.00
HETATM 14 CAN DR0 1 71.598 47.212 28.208 1.00 0.00
HETATM 15 OAO DR0 1 72.440 48.255 27.735 1.00 0.00
HETATM 16 OAP DR0 1 72.374 46.050 28.399 1.00 0.00
HETATM 17 CAA DRG 2 72.093 46.197 36.714 1.00 0.00
HETATM 18 CAB DRG 2 71.418 45.759 35.400 1.00 0.00
HETATM 19 CAC DRG 2 71.084 46.901 34.417 1.00 0.00
HETATM 20 CAD DRG 2 70.620 46.251 33.139 1.00 0.00
HETATM 21 CAE DRG 2 70.650 47.255 32.000 1.00 0.00
HETATM 22 CAF DRG 2 69.655 46.512 30.955 1.00 0.00
HETATM 23 CAG DRG 2 69.081 47.504 29.843 1.00 0.00
HETATM 24 CAH DRG 2 67.208 47.518 29.256 1.00 0.00
HETATM 25 CAI DRG 2 65.298 47.601 29.691 1.00 0.00
HETATM 26 CAJ DRG 2 65.629 48.362 30.827 1.00 0.00
HETATM 27 OAK DRG 2 65.140 49.590 30.429 1.00 0.00
HETATM 28 OAL DRG 2 64.837 47.815 31.709 1.00 0.00
HETATM 29 CAM DRG 2 63.041 47.557 29.333 1.00 0.00
HETATM 30 CAN DRG 2 62.808 47.023 27.931 1.00 0.00
HETATM 31 OAO DRG 2 63.130 48.142 27.185 1.00 0.00
HETATM 32 OAP DRG 2 63.560 45.894 27.706 1.00 0.00
HETATM 33 CAA DRG 3 61.174 46.188 36.668 1.00 0.00
HETATM 34 CAB DRG 3 60.510 45.777 35.344 1.00 0.00
HETATM 35 CAC DRG 3 60.221 46.928 34.352 1.00 0.00
HETATM 36 CAD DRG 3 59.724 46.337 32.998 1.00 0.00
HETATM 37 CAE DRG 3 60.252 47.307 31.985 1.00 0.00
HETATM 38 CAF DRG 3 61.089 46.606 30.881 1.00 0.00
HETATM 39 CAG DRG 3 60.868 47.564 29.740 1.00 0.00
HETATM 40 CAH DRG 3 58.621 47.652 29.253 1.00 0.00
HETATM 41 CAI DRG 3 56.328 47.703 29.755 1.00 0.00
HETATM 42 CAJ DRG 3 55.914 48.516 30.963 1.00 0.00
HETATM 43 OAK DRG 3 55.050 49.545 30.403 1.00 0.00
HETATM 44 OAL DRG 3 54.945 47.724 31.565 1.00 0.00
HETATM 45 CAM DRG 3 54.420 47.478 29.367 1.00 0.00
HETATM 46 CAN DRG 3 53.587 47.142 27.983 1.00 0.00
HETATM 47 OAO DRG 3 52.713 48.009 27.325 1.00 0.00
HETATM 48 OAP DRG 3 53.396 45.805 27.517 1.00 0.00
HETATM 49 CAA DR1 4 50.257 46.173 36.646 1.00 0.00
HETATM 50 CAB DR1 4 49.673 45.778 35.270 1.00 0.00
HETATM 51 CAC DR1 4 49.360 46.939 34.273 1.00 0.00
HETATM 52 CAD DR1 4 49.270 46.480 32.735 1.00 0.00
HETATM 53 CAE DR1 4 50.289 47.086 31.602 1.00 0.00
HETATM 54 CAF DR1 4 51.813 46.713 31.234 1.00 0.00
HETATM 55 CAG DR1 4 52.487 47.720 29.966 1.00 0.00
HETATM 56 CAH DR1 4 50.870 47.989 29.178 1.00 0.00
HETATM 57 CAI DR1 4 48.982 47.816 29.191 1.00 0.00
HETATM 58 CAJ DR1 4 47.901 48.319 30.192 1.00 0.00
HETATM 59 OAK DR1 4 47.004 49.132 29.503 1.00 0.00
HETATM 60 OAL DR1 4 46.963 47.171 30.588 1.00 0.00
HETATM 61 CAM DR1 4 47.752 46.922 28.157 1.00 0.00
HETATM 62 CAN DR1 4 46.372 47.149 27.020 1.00 0.00
HETATM 63 OAO DR1 4 45.018 47.950 26.877 1.00 0.00
HETATM 64 OAP DR1 4 46.019 46.082 26.137 1.00 0.00
TER
ENDMDL
--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
>
>
> nicegromacs wrote:
>> I follow some of the step of
>> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
>> omitted the change in the .hdb file because I don't have explicit
>> hydrogens). Well, I build a polymer with 3 units. The head (H), one
>> repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok,
>> but when I add one more repetitive unit (H-R-R-T) I get the following
>> error:
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: ../../../../src/kernel/pgutil.c, line: 87
>> Fatal error:
>> Atom CAM not found in residue 1083339441 while adding improper
>>
>> -------------------------------------------------------
>>
>
> It looks like pdb2gmx is finding some kind of undefined residue. Can you
> post the .pdb file?
>
> -Justin
>
>> "Stop Drinking My Beer !" (The Amps)
>>
>>
>>>
>>>
>>> nicegromacs wrote:
>>>
>>>> CAG -CAM
>>>
>>> Defining a bond to a previous residue will certainly fail for at least
>>> one terminus of your polymer chain. You may find this post useful:
>>>
>>> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
>>>
>>> If things still aren't working, please post the structure file, as well,
>>> and identify the bond that is being formed that shouldn't.
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> _______________________________________________
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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
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